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Description: Set sprai libexec path and blast path for system-wide installation
Author: Afif Elghraoui <afif@debian.org>
Forwarded: not-needed
Last-Update: 2016-06-01
--- sprai.orig/ezez4qsub_vx1.pl
+++ sprai/ezez4qsub_vx1.pl
@@ -117,8 +117,8 @@
my $trim="";
my $estimated_genome_size="";
my $ca_path="";
-my $blast_path="";
-my $sprai_path="";
+my $blast_path="/usr/bin";
+my $sprai_path="/usr/lib/sprai";
my $queue_req="";
my $longestXx_queue_req="";
my $blast_rreq="";
--- sprai.orig/ezez_vx1.pl
+++ sprai/ezez_vx1.pl
@@ -9,7 +9,7 @@
my $opt_dryrun;
my $opt_ec_only;
my $opt_foobar;
-my $sprai_path="";
+my $sprai_path="/usr/lib/sprai";
my $blast_path="";
my $now = `date +%Y%m%d_%H%M%S`;
--- sprai.orig/ec.spec
+++ sprai/ec.spec
@@ -11,6 +11,8 @@
estimated_depth 100
# ca_path: where Celera Assembler exist in
+# If you don't have it and only want to run error-correction,
+# don't set this variable (comment it out)
ca_path /home/imai/wgs/Linux-amd64/bin/
# the number of processes used by all vs. all alignment
@@ -19,13 +21,6 @@
pre_partition 2
partition 12
-# sprai prefer full paths
-# if you use ezez4qsub*.pl. you MUST specify blast_path & sprai_path
-# blast_path: where blastn and makeblastdb exist in
-blast_path /home/imai/bin/
-# sprai_path: where binaries of sprai (bfmt72s, nss2v_v3 and so on) exist in
-sprai_path /home/imai/test/sprai/bin/
-
#### many node mode (advanced) ####
#sge: options for all the SGE jobs (used by ezez4qsub_vx1.pl)
--- sprai.orig/ezez4makefile_v4.pl
+++ sprai/ezez4makefile_v4.pl
@@ -84,8 +84,8 @@
my $estimated_depth = 0;
my @gsizes=();
my $ca_path="/opt/wgs-8.1/Linux-amd64/bin/";
-my $blast_path="/usr/local/bin/";
-my $sprai_path="/usr/local/bin/";
+my $blast_path="/usr/bin/";
+my $sprai_path="/usr/lib/sprai/";
my $param_makedb_rreq = ""; # not so much resource
my $param_blast_rreq = ""; # desired to have a high CPU slot for latency optimization
my $param_ec_rreq = ""; # not so much resource
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